Author: laylaoesper
Date: 2010-07-12 05:58:22 -0700 (Mon, 12 Jul 2010)
New Revision: 20902
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudParameters.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummary.jar
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryInputPanel.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryManager.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryParameters.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryPlugin.java
Log:
Move the word exclusion to the network level for Semantic Summary Plugin.
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudParameters.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudParameters.java
2010-07-12 03:18:16 UTC (rev 20901)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudParameters.java
2010-07-12 12:58:22 UTC (rev 20902)
@@ -74,7 +74,6 @@
private HashMap<String, Double> pairRatios;
private ArrayList<CloudWordInfo> cloudWords;
- private WordFilter filter;
private Double netWeightFactor;
private Double clusterCutoff;
@@ -112,7 +111,6 @@
this.ratios = new HashMap<String, Double>();
this.pairRatios = new HashMap<String, Double>();
this.cloudWords = new ArrayList<CloudWordInfo>();
- this.filter = new WordFilter();
this.netWeightFactor = this.getDefaultNetWeight();
this.attributeName = this.getDefaultAttName();
@@ -226,6 +224,7 @@
String curWord = wordIter.next();
//Check filters
+ WordFilter filter = networkParams.getFilter();
if (!filter.contains(curWord))
{
//If this word has not been
encountered, or not encountered
@@ -321,6 +320,7 @@
String curWord = wordIter.next();
//Check filters
+ WordFilter filter = networkParams.getFilter();
if (!filter.contains(curWord))
{
//Add to selected Counts
@@ -1054,17 +1054,7 @@
networkNumNodes = num;
}
- public WordFilter getFilter()
- {
- return filter;
- }
- public void setFilter(WordFilter aFilter)
- {
- filter = aFilter;
- }
-
-
public Double getMinRatio()
{
return minRatio;
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummary.jar
===================================================================
(Binary files differ)
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryInputPanel.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryInputPanel.java
2010-07-12 03:18:16 UTC (rev 20901)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryInputPanel.java
2010-07-12 12:58:22 UTC (rev 20902)
@@ -685,7 +685,8 @@
cmb.removeAllElements();
CloudParameters params =
SemanticSummaryManager.getInstance().getCurCloud();
- WordFilter curFilter = params.getFilter();
+ SemanticSummaryParameters networkParams =
params.getNetworkParams();
+ WordFilter curFilter = networkParams.getFilter();
//Check if we are dealing with the Null CloudParameters
Boolean isNull = false;
@@ -937,7 +938,8 @@
!selectItem.equalsIgnoreCase(stopSeparator))
{
CloudParameters params =
SemanticSummaryManager.getInstance().getCurCloud();
- WordFilter curFilter =
params.getFilter();
+ SemanticSummaryParameters
networkParams = params.getNetworkParams();
+ WordFilter curFilter =
networkParams.getFilter();
//Remove from filter
curFilter.remove(selectItem);
@@ -963,7 +965,8 @@
{
//add value to cloud parameters filter
and update
CloudParameters params =
SemanticSummaryManager.getInstance().getCurCloud();
- WordFilter curFilter =
params.getFilter();
+ SemanticSummaryParameters networkParams
= params.getNetworkParams();
+ WordFilter curFilter =
networkParams.getFilter();
value.toLowerCase();
curFilter.add(value);
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryManager.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryManager.java
2010-07-12 03:18:16 UTC (rev 20901)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryManager.java
2010-07-12 12:58:22 UTC (rev 20902)
@@ -77,6 +77,7 @@
nullSemanticSummary.setNetworkName("No Network Loaded");
nullCloudParameters = new CloudParameters();
nullCloudParameters.setCloudName("Null Cloud");
+ nullCloudParameters.setNetworkParams(nullSemanticSummary);
//catch network creation/destruction events
Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(this);
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryParameters.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryParameters.java
2010-07-12 03:18:16 UTC (rev 20901)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryParameters.java
2010-07-12 12:58:22 UTC (rev 20902)
@@ -61,6 +61,8 @@
//String Delimeters
private static final String NODEDELIMITER = "SSParamNodeDelimiter";
+ private WordFilter filter;
+
//CONSTRUCTORS
/**
@@ -70,6 +72,7 @@
{
this.clouds = new HashMap<String,CloudParameters>();
this.nodeList = new ArrayList<String>();
+ this.filter = new WordFilter();
}
/**
@@ -363,4 +366,14 @@
{
return SEPARATER;
}
+
+ public WordFilter getFilter()
+ {
+ return filter;
+ }
+
+ public void setFilter(WordFilter aFilter)
+ {
+ filter = aFilter;
+ }
}
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryPlugin.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryPlugin.java
2010-07-12 03:18:16 UTC (rev 20901)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryPlugin.java
2010-07-12 12:58:22 UTC (rev 20902)
@@ -152,6 +152,12 @@
writer.write(params.toString());
writer.close();
+ File current_filter = new File(tmpDir,
netNameSep + networkName + netNameSep + ".FILTER.txt");
+ BufferedWriter filterWriter = new
BufferedWriter(new FileWriter(current_filter));
+
filterWriter.write(params.getFilter().toString());
+ filterWriter.close();
+ pFileList.add(current_filter);
+
//Loop on Clouds
if (!params.getClouds().isEmpty())
{
@@ -227,15 +233,6 @@
subCloud8Writer.close();
pFileList.add(current_pairRatios);
- //File for Filter
- File current_filter = new
File(tmpDir, netNameSep + networkName + netNameSep +
- cloudNameSep +
cloud_name + cloudNameSep + ".FILTER.txt");
- BufferedWriter subCloud9Writer
= new BufferedWriter(new FileWriter(current_filter));
-
subCloud9Writer.write(cloud.getFilter().toString());
- subCloud9Writer.close();
- pFileList.add(current_filter);
-
-
}//end iteration over clouds
}//end if clouds exist for network
}//end try
@@ -294,7 +291,7 @@
}//end if .props file
}//end loop through all props files
- //Go through the prop files to create the clouds
+ //Go through the prop files to create the clouds and
set filters
for (int i = 0; i < pStateFileList.size(); i++)
{
File prop_file = pStateFileList.get(i);
@@ -324,6 +321,25 @@
networkParams.addCloud(cloud_name,
params);
}//end if .CLOUDS.txt file
+
+ if (prop_file.getName().contains(".FILTER.txt"))
+ {
+ TextFileReader reader = new
TextFileReader(prop_file.getAbsolutePath());
+ reader.read();
+ String fullText = reader.getText();
+
+ //Get the networkID from the props file
+ String[] fullname =
prop_file.getName().split(netNameSep);
+ String net_name = fullname[1];
+
+ //Get the Network Parameters
+ SemanticSummaryParameters networkParams
=
+
SemanticSummaryManager.getInstance().getCyNetworkList().get(net_name);
+
+ //Recreate the Filter and set pointer
in cloud
+ WordFilter curFilter = new
WordFilter(fullText);
+ networkParams.setFilter(curFilter);
+ }
}//end loop through all props files
@@ -333,7 +349,8 @@
File prop_file = pStateFileList.get(i);
if (prop_file.getName().contains(".CLOUDS.txt")
||
-
prop_file.getName().contains(".props"))
+
prop_file.getName().contains(".props") ||
+
prop_file.getName().contains(".FILTER.txt"))
continue;
TextFileReader reader = new
TextFileReader(prop_file.getAbsolutePath());
@@ -405,12 +422,6 @@
cloudParams.setPairRatios(pairRatios);
}
- if (prop_file.getName().contains(".FILTER.txt"))
- {
- //Recreate the Filter and set pointer
in cloud
- WordFilter curFilter = new
WordFilter(fullText);
- cloudParams.setFilter(curFilter);
- }
}//end loop through all props files
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